// =================================================================================
// Set the attributes of the primary field variables
// =================================================================================
// This function sets attributes for each variable/equation in the app. The
// attributes are set via standardized function calls. The first parameter for each
// function call is the variable index (starting at zero). The first set of
// variable/equation attributes are the variable name (any string), the variable
// type (SCALAR/VECTOR), and the equation type (EXPLICIT_TIME_DEPENDENT/
// TIME_INDEPENDENT/AUXILIARY). The next set of attributes describe the
// dependencies for the governing equation on the values and derivatives of the
// other variables for the value term and gradient term of the RHS and the LHS.
// The final pair of attributes determine whether a variable represents a field
// that can nucleate and whether the value of the field is needed for nucleation
// rate calculations.

void variableAttributeLoader::loadVariableAttributes(){
	// Variable 0
	set_variable_name				(0,"c");
	set_variable_type				(0,SCALAR);
	set_variable_equation_type		(0,EXPLICIT_TIME_DEPENDENT);

    set_dependencies_value_term_RHS(0, "c");
    set_dependencies_gradient_term_RHS(0, "grad(mu)");

	// Variable 1
	set_variable_name				(1,"mu");
	set_variable_type				(1,SCALAR);
	set_variable_equation_type		(1,AUXILIARY);

    set_dependencies_value_term_RHS(1, "c, phi");
    set_dependencies_gradient_term_RHS(1, "grad(c)");

    // Variable 2
    set_variable_name				(2,"phi");
    set_variable_type				(2,SCALAR);
    set_variable_equation_type		(2,TIME_INDEPENDENT);

    set_dependencies_value_term_RHS(2, "c");
    set_dependencies_gradient_term_RHS(2, "grad(phi)");
    set_dependencies_value_term_LHS(2, "");
    set_dependencies_gradient_term_LHS(2, "grad(change(phi))");

}

// =============================================================================================
// explicitEquationRHS (needed only if one or more equation is explict time dependent)
// =============================================================================================
// This function calculates the right-hand-side of the explicit time-dependent
// equations for each variable. It takes "variable_list" as an input, which is a list
// of the value and derivatives of each of the variables at a specific quadrature
// point. The (x,y,z) location of that quadrature point is given by "q_point_loc".
// The function outputs two terms to variable_list -- one proportional to the test
// function and one proportional to the gradient of the test function. The index for
// each variable in this list corresponds to the index given at the top of this file.

template <int dim, int degree>
void customPDE<dim,degree>::explicitEquationRHS(variableContainer<dim,degree,dealii::VectorizedArray<double> > & variable_list,
				 dealii::Point<dim, dealii::VectorizedArray<double> > q_point_loc) const {

// --- Getting the values and derivatives of the model variables ---

// The concentration and its derivatives
scalarvalueType c = variable_list.get_scalar_value(0);

// The chemical potential and its derivatives
scalargradType mux = variable_list.get_scalar_gradient(1);

// --- Setting the expressions for the terms in the governing equations ---

// The terms in the equations
scalarvalueType eq_c = c;
scalargradType eqx_c = constV(-McV*userInputs.dtValue)*mux;

// --- Submitting the terms for the governing equations ---

variable_list.set_scalar_value_term_RHS(0,eq_c);
variable_list.set_scalar_gradient_term_RHS(0,eqx_c);

}

// =============================================================================================
// nonExplicitEquationRHS (needed only if one or more equation is time independent or auxiliary)
// =============================================================================================
// This function calculates the right-hand-side of all of the equations that are not
// explicit time-dependent equations. It takes "variable_list" as an input, which is
// a list of the value and derivatives of each of the variables at a specific
// quadrature point. The (x,y,z) location of that quadrature point is given by
// "q_point_loc". The function outputs two terms to variable_list -- one proportional
// to the test function and one proportional to the gradient of the test function. The
// index for each variable in this list corresponds to the index given at the top of
// this file.

template <int dim, int degree>
void customPDE<dim,degree>::nonExplicitEquationRHS(variableContainer<dim,degree,dealii::VectorizedArray<double> > & variable_list,
				 dealii::Point<dim, dealii::VectorizedArray<double> > q_point_loc) const {

 // --- Getting the values and derivatives of the model variables ---

 scalarvalueType c = variable_list.get_scalar_value(0);
 scalargradType cx = variable_list.get_scalar_gradient(0);

 // The electric potential and its derivatives
 scalarvalueType phi = variable_list.get_scalar_value(2);
 scalargradType phix = variable_list.get_scalar_gradient(2);

 // --- Setting the expressions for the terms in the governing equations ---

 // The derivative of the local chemical free energy
 scalarvalueType fcV = 2.0*rho*(c-c_alpha)*(c_beta-c)*(c_alpha+c_beta-2.0*c);

 // The derivative of the local electrostatic free energy
 scalarvalueType fphiV = k*phi;

 scalarvalueType eq_mu = fcV+fphiV;
 scalargradType eqx_mu = constV(KcV)*cx;
 scalarvalueType eq_phi = -constV(-k/epsilon)*c;
 scalargradType eqx_phi = -phix;

 // --- Submitting the terms for the governing equations ---

 variable_list.set_scalar_value_term_RHS(1,eq_mu);
 variable_list.set_scalar_gradient_term_RHS(1,eqx_mu);

 variable_list.set_scalar_value_term_RHS(2,eq_phi);
 variable_list.set_scalar_gradient_term_RHS(2,eqx_phi);


}

// =============================================================================================
// equationLHS (needed only if at least one equation is time independent)
// =============================================================================================
// This function calculates the left-hand-side of time-independent equations. It
// takes "variable_list" as an input, which is a list of the value and derivatives of
// each of the variables at a specific quadrature point. The (x,y,z) location of that
// quadrature point is given by "q_point_loc". The function outputs two terms to
// variable_list -- one proportional to the test function and one proportional to the
// gradient of the test function -- for the left-hand-side of the equation. The index
// for each variable in this list corresponds to the index given at the top of this
// file. If there are multiple elliptic equations, conditional statements should be
// sed to ensure that the correct residual is being submitted. The index of the field
// being solved can be accessed by "this->currentFieldIndex".

template <int dim, int degree>
void customPDE<dim,degree>::equationLHS(variableContainer<dim,degree,dealii::VectorizedArray<double> > & variable_list,
		dealii::Point<dim, dealii::VectorizedArray<double> > q_point_loc) const {

// --- Getting the values and derivatives of the model variables ---

//grad(delta phi)
scalargradType Dphix = variable_list.get_change_in_scalar_gradient(2);

// --- Setting the expressions for the terms in the governing equations ---

scalargradType eqx_Dphi=Dphix;

 // --- Submitting the terms for the governing equations ---

variable_list.set_scalar_gradient_term_LHS(2,eqx_Dphi);

}
